[netCDF #TYA-988003]: Compilation of NetCDF

Hi Nicolas,

For netcdf-4.3.0 (and any netCDF version since 4.1.2 from 2011), the 
"--with-hdf5=..." is not a supported configure option.  Instead, you 
need to specify the location of the installed HDF5 library with the 
environment variables CPPFLAGS and LDFLAGS, as described here:

  http://www.unidata.ucar.edu/netcdf/docs/build_default.html

If you're intrested, the reasons for dropping the use of the with-hdf5= 
option are explained here:

  
http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2011/msg00345.html

Also, buiding and installing the netcdf-fortran 4.2 library depends on 
first installing the netCDF C library, currently at version 4.3.0, as
described here:

  http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html

Compiling with parallel access enabled depends on the HDF5 library having 
been built with parallel access, and the use of parallel compilers, as you
have specified:

  http://www.unidata.ucar.edu/netcdf/docs/build_parallel.html

Good luck, and let us know if you encounter additional problems with the
build.

--Russ

> I'm trying to compile netcdf-4 with parallel access enabled.
> So I'm using the intel composer XE suite 2013 (composer_xe_2013_sp1) but
> can't compile the netcdf lib... here are my commands :
> 
> # the C compiler (Composer XE suite)
> export CC=mpiicc
> # the C++ compiler, the intel one.
> export CXX=mpiicpc
> # the Fortran 9X compiler.
> export FC=mpiifort
> # the Fortran 77 compiler. For intel, is just the fortran one.
> export F77=mpif77
> # C Compiler flags
> export CFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
> # F9X Compiler flags
> export FCFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
> # F77 Compiler flags
> export FFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
> # CXX Compiler flags
> export CXXFLAGS="-O3 -xHost -axSSE4.2 -fPIC"
> # Linker flags
> export LDFLAGS="-Wl,-rpath=/opt/intel/lib
> -Wl,-rpath=/opt/intel/lib/intel64 -i-dynamic"
> 
> Zlib (compiled successfully) :
> 
> wget
> downloads.sourceforge.net/project/libpng/zlib/1.2.8/zlib-1.2.8.tar.gz
> tar -xvf zlib-1.2.8.tar.gz
> cd zlib-1.2.8
> ./configure --prefix=/home/OASIS/nnajdovski/local/zlib --64
> make clean; make all check install
> cd ../
> 
> HDF5 (compiled successfully) :
> 
> wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12.tar.gz
> tar -xvf hdf5-1.8.12.tar.gz
> cd hdf5-1.8.12/
> ./configure --prefix=/home/OASIS/nnajdovski/local/hdf5
> --enable-fortran --with-zlib=/home/OASIS/nnajdovski/local/
> --enable-parallel
> make clean; make all check install
> cd ../
> 
> SUMMARY OF THE HDF5 CONFIGURATION
> =================================
> 
> General Information:
> -------------------
> HDF5 Version: 1.8.12
> Configured on: Mon Nov 25 09:26:12 CET 2013
> Configured by: nnajdovski@eliegeo09
> Configure mode: production
> Host system: x86_64-unknown-linux-gnu
> Uname information: Linux eliegeo09 3.4.63-2.44-desktop #1 SMP
> PREEMPT Wed Oct 2 11:18:32 UTC 2013 (d91a619) x86_64 x86_64
> x86_64 GNU/Linux
> Byte sex: little-endian
> Libraries: static
> Installation point: /home/OASIS/nnajdovski/local/hdf5
> 
> Compiling Options:
> ------------------
> Compilation Mode: production
> C Compiler: /opt/intel/impi/4.1.1.036/bin64/mpiicc ( Intel(R) C
> Intel(R) 64 Compiler Version 14.0.0.080 Build 20130728)
> CFLAGS: -O3 -xHost -axSSE4.2 -fPIC
> H5_CFLAGS: -std=c99  -O
> AM_CFLAGS:
> CPPFLAGS:
> H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API
> AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
> -D_BSD_SOURCE
> Shared C Library: no
> Static C Library: yes
> Statically Linked Executables: no
> LDFLAGS: -Wl,-rpath=/opt/intel/lib
> -Wl,-rpath=/opt/intel/lib/intel64 -i-dynamic
> H5_LDFLAGS:
> AM_LDFLAGS:
> Extra libraries:  -lz -ldl -lm
> Archiver: ar
> Ranlib: ranlib
> Debugged Packages:
> API Tracing: no
> 
> Languages:
> ----------
> Fortran: yes
> Fortran Compiler: /opt/intel/impi/4.1.1.036/bin64/mpiifort (
> Intel(R) Fortran Intel(R) 64 Compiler Version 14.0.0.080 Build
> 20130728)
> Fortran 2003 Compiler: no
> Fortran Flags: -O3 -xHost -axSSE4.2 -fPIC
> H5 Fortran Flags:  -O3
> AM Fortran Flags:
> Shared Fortran Library: no
> Static Fortran Library: yes
> 
> C++: no
> 
> Features:
> ---------
> Parallel HDF5: yes
> High Level library: yes
> Threadsafety: no
> Default API Mapping: v18
> With Deprecated Public Symbols: yes
> I/O filters (external): deflate(zlib)
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
> MPE:
> Direct VFD: no
> dmalloc: no
> Clear file buffers before write: yes
> Using memory checker: no
> Function Stack Tracing: no
> GPFS: no
> Strict File Format Checks: no
> Optimization Instrumentation: no
> Large File Support (LFS): yes
> 
> 
> NETCDF-4 (Compilation failed) :
> 
> wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.0.tar.gz
> tar -xvf netcdf-4.3.0.tar.gz
> cd netcdf-4.3.0/
> ./configure --prefix=/home/OASIS/nnajdovski/local/netcdf
> --with-hdf5=/home/OASIS/nnajdovski/local/hdf5/ --enable-fortran=yes
> --enable-netcdf4=yes
> make clean; make check install -j 2
> export
> LD_LIBRARY_PATH=/home/OASIS/nnajdovski/local/netcdf/lib:$LD_LIBRARY_PATH
> 
> configure: WARNING: unrecognized options: --with-hdf5
> configure: loading site script
> /usr/share/site/x86_64-unknown-linux-gnu
> 
> 
> cd ../
> wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.2.tar.gz
> tar -xvf netcdf-4.2.tar.gz
> cd netcdf-fortran-4.2/
> CPPFLAGS=-I/home/OASIS/nnajdovski/local/netcdf/include
> LDFLAGS=-L/home/OASIS/nnajdovski/local/netcdf/lib ./configure
> --prefix=/home/OASIS/nnajdovski/local/netcdf
> --with-hdf5=/home/OASIS/nnajdovski/local/hdf5/ --enable-netcdf4=yes
> make clean; make check install -j 2
> 
> configure: WARNING: unrecognized options: --with-hdf5,
> --enable-netcdf4
> 
> cd .. && /bin/sh ./config.status fortran/nfconfig1.inc
> fort-nc4.c(204): warning #167: argument of type "const int *" is
> incompatible with parameter of type "const long long *"
> FCALLSCFUN4(NF_INT, nc_put_var1_longlong, NF_PUT_VAR1_INT64,
> nf_put_var1_int64,
> ^
> 
> fort-nc4.c(206): warning #167: argument of type "const int *" is
> incompatible with parameter of type "const long long *"
> FCALLSCFUN5(NF_INT, nc_put_vara_longlong, NF_PUT_VARA_INT64,
> nf_put_vara_int64,
> ^
> 
> fort-nc4.c(208): warning #167: argument of type "const int *" is
> incompatible with parameter of type "const long long *"
> FCALLSCFUN6(NF_INT, nc_put_vars_longlong, NF_PUT_VARS_INT64,
> nf_put_vars_int64,
> ^
> 
> fort-nc4.c(210): warning #167: argument of type "int *" is
> incompatible with parameter of type "const long long *"
> FCALLSCFUN7(NF_INT, nc_put_varm_longlong, NF_PUT_VARM_INT64,
> nf_put_varm_int64,
> ^
> 
> fort-nc4.c(212): warning #167: argument of type "int *" is
> incompatible with parameter of type "const long long *"
> FCALLSCFUN3(NF_INT, nc_put_var_longlong, NF_PUT_VAR_INT64,
> nf_put_var_int64,
> ^
> 
> fort-nc4.c(215): warning #2330: argument of type "const int *"
> is incompatible with parameter of type "long long *" (dropping
> qualifiers)
> FCALLSCFUN4(NF_INT, nc_get_var1_longlong, NF_GET_VAR1_INT64,
> nf_get_var1_int64,
> ^
> 
> fort-nc4.c(217): warning #2330: argument of type "const int *"
> is incompatible with parameter of type "long long *" (dropping
> qualifiers)
> FCALLSCFUN5(NF_INT, nc_get_vara_longlong, NF_GET_VARA_INT64,
> nf_get_vara_int64,
> ^
> 
> fort-nc4.c(219): warning #2330: argument of type "const int *"
> is incompatible with parameter of type "long long *" (dropping
> qualifiers)
> FCALLSCFUN6(NF_INT, nc_get_vars_longlong, NF_GET_VARS_INT64,
> nf_get_vars_int64,
> ^
> 
> fort-nc4.c(221): warning #167: argument of type "int *" is
> incompatible with parameter of type "long long *"
> FCALLSCFUN7(NF_INT, nc_get_varm_longlong, NF_GET_VARM_INT64,
> nf_get_varm_int64,
> ^
> 
> fort-nc4.c(223): warning #167: argument of type "int *" is
> incompatible with parameter of type "long long *"
> FCALLSCFUN3(NF_INT, nc_get_var_longlong, NF_GET_VAR_INT64,
> nf_get_var_int64,
> ^
> 
> config.status: creating fortran/nfconfig1.inc
> make[3] : on quitte le répertoire «
> /home/OASIS/nnajdovski/local/netcdf-fortran-4.2/fortran »
> libtool: compile:  mpiicc -DHAVE_CONFIG_H -I. -I.. -DDLL_EXPORT
> -I/home/OASIS/nnajdovski/local/netcdf/include -O3 -xHost
> -axSSE4.2 -fPIC -MT fort-nc4.lo -MD -MP -MF .deps/fort-nc4.Tpo
> -c fort-nc4.c -o fort-nc4.o >/dev/null 2>&1
> /bin/sh ../libtool --tag=FC   --mode=link mpiifort  -O3 -xHost
> -axSSE4.2 -fPIC  -version-number 5:3:1
> -L/home/OASIS/nnajdovski/local/netcdf/lib -o libnetcdff.la
> -rpath /home/OASIS/nnajdovski/local/netcdf/lib64 fort-attio.lo
> fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo
> fort-genvar.lo fort-lib.lo fort-misc.lo fort-v2compat.lo
> fort-vario.lo fort-var1io.lo fort-varaio.lo fort-varmio.lo
> fort-varsio.lo fort-nc4.lo ../f90/libnetcdff90.la -lnetcdf
> libtool: link: mpiifort -shared  .libs/fort-attio.o
> .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o
> .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o
> .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o
> .libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o
> .libs/fort-varsio.o .libs/fort-nc4.o   --whole-archive
> ../f90/.libs/libnetcdff90.a --no-whole-archive
> -L/home/OASIS/nnajdovski/local/netcdf/lib -lnetcdf -soname
> libnetcdff.so.5 -o .libs/libnetcdff.so.5.3.1
> ifort: command line warning #10006: ignoring unknown option
> '-fwhole-archive'
> ifort: command line warning #10006: ignoring unknown option
> '-fno-whole-archive'
> ifort: command line warning #10006: ignoring unknown option
> '-soname'
> *ifort: error #10236: File not found:  'libnetcdff.so.5'*
> make[2]: *** [libnetcdff.la] Erreur 1
> make[2] : on quitte le répertoire «
> /home/OASIS/nnajdovski/local/netcdf-fortran-4.2/fortran »
> make[1]: *** [install] Erreur 2
> make[1] : on quitte le répertoire «
> /home/OASIS/nnajdovski/local/netcdf-fortran-4.2/fortran »
> make: *** [install-recursive] Erreur 1
> 
> 
> What am I doing wrong?
> 
> Thanks,
> 
> Best,
> Nicolas
> 
> 
> 
> 
> --
> 
> 
> 
> *
> NAJDOVSKI Nicolas - PhD Student
> **Earthand Life Institute <http://www.uclouvain.be/eli>***/-
> //Environment <http://www.uclouvain.be/elie>/
> Université catholique de Louvain <http://www.uclouvain.be>
> Croix du Sud, 2 - L7.05.16
> 1348 Louvain-la-Neuve, Belgium
> Tél +32 (0) 10 47 88 97
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: TYA-988003
Department: Support netCDF
Priority: Normal
Status: Closed